When searching for people in Japan, prepare yourself for disappointment. Searching for a friend makes the task somewhat less daunting, especially if your friend participates in online social networks, has a homepage, or, in general, wants to be locatable. If these points do not apply to your friend, then your best bet is to post ads in newspapers and contact their family members or associates. As a last ditch measure, you may attempt to go through government agencies, but for this you will need the person's "jyuminkihondaichou" number (citizen ID number), providing your friend is Japanese and has volunteered to participate in this system.
Online and Newspapers
Search for your friend on Facebook, Myspace, Yahoo, or Google; Mixi is one of the more popular social networking sites in Japan, so try there as well, especially if your friend is Japanese. Conduct this search in English and Japanese, using names, nicknames, and email addresses whenever possible.
Post a request for information on an online message board for people searching for persons in Japan. There are many such sites, primarily due to the near-impossibility of independently conducting such a search from outside Japan. Provide as much information about your friend as possible: name (in kanji, if possible), age, sex, last-known address, place of work, etc.
Find an online edition of a major Japanese newspaper: The Daily Yomiyuri, The Asahi Shinbun, or The Japan Times should do. Contact their classifieds department and inquire about posting a notification that you are seeking a person. If the price is within your range, confirm how to post such an advertisement.
Place the advertisement, providing the persons name and last known location or employer. Many people in Japan have the same or very similar names, so providing additional information will help narrow your search.
Word of Mouth
Contact anyone who knew your friend. Word-of-mouth searches provide your second-best chance of success. Family members, friends, and former coworkers will be able to provide you with information much more readily than public officials.
Contact the appropriate embassy or consulate. In most cases, the government officials are not empowered to officially help you locate a person of non-Japanese origin in Japan, but they may be able to point you in the direction of someone who can.
If possible, contact your friend's last known employer. Former coworkers may be able to provide you with some information.
National Registry System
Submit an application for locating an individual in the "jyuminkihondaichou" network system. You will need to do this at the city or ward office. You must provide a legitimate reason for this search. Government officials will judge whether your request is legitimate or not before sending the paperwork onto the proper office.
Provide the officials your friend's "juki-net" (as the national registry is commonly called) number. The juki-net number will be an 11-digit number. These numbers are not available online, and there is no way to conduct an online search for these numbers.
Continue pursuing other avenues of inquiry. Your "juki-net" search will probably have no success. The "juki-net" system carries minimal data (name, date-of-birth, sex, and address), but is entirely voluntary; in most places in Japan, less than half of the citizens have opted to join the system.